4YB4
Crystal structure of homoisocitrate dehydrogenase from Thermus thermophilus in complex with homoisocitrate, magnesium ion (II) and NADH
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004449 | molecular_function | isocitrate dehydrogenase (NAD+) activity |
| A | 0009085 | biological_process | lysine biosynthetic process |
| A | 0016491 | molecular_function | oxidoreductase activity |
| A | 0019878 | biological_process | lysine biosynthetic process via aminoadipic acid |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0047046 | molecular_function | homoisocitrate dehydrogenase activity |
| B | 0004449 | molecular_function | isocitrate dehydrogenase (NAD+) activity |
| B | 0009085 | biological_process | lysine biosynthetic process |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0019878 | biological_process | lysine biosynthetic process via aminoadipic acid |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0047046 | molecular_function | homoisocitrate dehydrogenase activity |
| C | 0004449 | molecular_function | isocitrate dehydrogenase (NAD+) activity |
| C | 0009085 | biological_process | lysine biosynthetic process |
| C | 0016491 | molecular_function | oxidoreductase activity |
| C | 0019878 | biological_process | lysine biosynthetic process via aminoadipic acid |
| C | 0046872 | molecular_function | metal ion binding |
| C | 0047046 | molecular_function | homoisocitrate dehydrogenase activity |
| D | 0004449 | molecular_function | isocitrate dehydrogenase (NAD+) activity |
| D | 0009085 | biological_process | lysine biosynthetic process |
| D | 0016491 | molecular_function | oxidoreductase activity |
| D | 0019878 | biological_process | lysine biosynthetic process via aminoadipic acid |
| D | 0046872 | molecular_function | metal ion binding |
| D | 0047046 | molecular_function | homoisocitrate dehydrogenase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 5 |
| Details | binding site for residue MG A 401 |
| Chain | Residue |
| A | ASP228 |
| A | 48Y402 |
| A | HOH563 |
| B | ASP204 |
| B | HOH582 |
| site_id | AC2 |
| Number of Residues | 18 |
| Details | binding site for residue 48Y A 402 |
| Chain | Residue |
| A | ARG118 |
| A | TYR125 |
| A | ASP228 |
| A | MG401 |
| A | NAI403 |
| A | HOH530 |
| A | HOH537 |
| A | HOH541 |
| A | HOH563 |
| B | LYS171 |
| B | ASN173 |
| B | VAL174 |
| B | ASP204 |
| B | HOH582 |
| A | SER72 |
| A | ARG85 |
| A | ARG88 |
| A | ARG98 |
| site_id | AC3 |
| Number of Residues | 29 |
| Details | binding site for residue NAI A 403 |
| Chain | Residue |
| A | ILE13 |
| A | PHE67 |
| A | ALA69 |
| A | ALA70 |
| A | THR71 |
| A | SER72 |
| A | LEU241 |
| A | GLU257 |
| A | HIS260 |
| A | GLY261 |
| A | SER262 |
| A | ALA263 |
| A | ASP265 |
| A | ILE266 |
| A | ASN273 |
| A | 48Y402 |
| A | HOH512 |
| A | HOH518 |
| A | HOH526 |
| A | HOH530 |
| A | HOH564 |
| A | HOH566 |
| A | HOH617 |
| A | HOH621 |
| B | ASN173 |
| B | ILE202 |
| B | ASN205 |
| B | GOL403 |
| B | HOH601 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | binding site for residue MG A 404 |
| Chain | Residue |
| A | ASP204 |
| B | ASP228 |
| B | 48Y401 |
| B | HOH584 |
| B | HOH585 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | binding site for residue GOL A 405 |
| Chain | Residue |
| A | MET208 |
| A | ARG213 |
| A | HOH615 |
| B | GLY240 |
| B | LEU241 |
| B | ASP313 |
| site_id | AC6 |
| Number of Residues | 5 |
| Details | binding site for residue GOL A 406 |
| Chain | Residue |
| A | LEU124 |
| A | GLN179 |
| A | THR223 |
| A | ASN224 |
| A | LEU225 |
| site_id | AC7 |
| Number of Residues | 2 |
| Details | binding site for residue GOL A 407 |
| Chain | Residue |
| A | ILE157 |
| A | ARG161 |
| site_id | AC8 |
| Number of Residues | 4 |
| Details | binding site for residue GOL A 408 |
| Chain | Residue |
| A | PRO99 |
| A | LEU279 |
| A | GLU298 |
| A | HOH612 |
| site_id | AC9 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 A 409 |
| Chain | Residue |
| A | ARG213 |
| A | HOH592 |
| site_id | AD1 |
| Number of Residues | 6 |
| Details | binding site for residue SO4 A 410 |
| Chain | Residue |
| A | ASP200 |
| A | ILE202 |
| A | HOH501 |
| A | HOH506 |
| B | THR74 |
| D | LYS269 |
| site_id | AD2 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 A 411 |
| Chain | Residue |
| A | PRO73 |
| A | THR74 |
| A | ARG75 |
| A | SO4415 |
| A | HOH619 |
| site_id | AD3 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 A 412 |
| Chain | Residue |
| A | TYR94 |
| A | ALA153 |
| A | ARG156 |
| site_id | AD4 |
| Number of Residues | 1 |
| Details | binding site for residue SO4 A 413 |
| Chain | Residue |
| A | ARG310 |
| site_id | AD5 |
| Number of Residues | 7 |
| Details | binding site for residue SO4 A 414 |
| Chain | Residue |
| A | TYR94 |
| A | ARG152 |
| A | ARG156 |
| A | HOH519 |
| A | HOH534 |
| A | HOH595 |
| A | HOH596 |
| site_id | AD6 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 A 415 |
| Chain | Residue |
| A | THR71 |
| A | SO4411 |
| A | HOH619 |
| A | TRP41 |
| site_id | AD7 |
| Number of Residues | 16 |
| Details | binding site for residue 48Y B 401 |
| Chain | Residue |
| A | LYS171 |
| A | ASN173 |
| A | VAL174 |
| A | ASP204 |
| A | MG404 |
| B | SER72 |
| B | ARG85 |
| B | ARG88 |
| B | ARG98 |
| B | ARG118 |
| B | TYR125 |
| B | ASP228 |
| B | NAI402 |
| B | HOH556 |
| B | HOH584 |
| B | HOH598 |
| site_id | AD8 |
| Number of Residues | 31 |
| Details | binding site for residue NAI B 402 |
| Chain | Residue |
| A | ASN173 |
| A | ILE202 |
| A | ASN205 |
| A | HOH615 |
| B | ILE13 |
| B | PHE67 |
| B | ALA70 |
| B | THR71 |
| B | SER72 |
| B | ILE84 |
| B | LEU241 |
| B | GLU257 |
| B | VAL259 |
| B | HIS260 |
| B | GLY261 |
| B | SER262 |
| B | ALA263 |
| B | PRO264 |
| B | ASP265 |
| B | ILE266 |
| B | ASN273 |
| B | 48Y401 |
| B | HOH530 |
| B | HOH531 |
| B | HOH534 |
| B | HOH549 |
| B | HOH559 |
| B | HOH586 |
| B | HOH600 |
| B | HOH611 |
| B | HOH620 |
| site_id | AD9 |
| Number of Residues | 7 |
| Details | binding site for residue GOL B 403 |
| Chain | Residue |
| A | GLY240 |
| A | LEU241 |
| A | ASP313 |
| A | NAI403 |
| B | MET208 |
| B | ARG213 |
| B | HOH601 |
| site_id | AE1 |
| Number of Residues | 5 |
| Details | binding site for residue GOL B 404 |
| Chain | Residue |
| B | GLY123 |
| B | LEU124 |
| B | GLN179 |
| B | THR223 |
| B | LEU225 |
| site_id | AE2 |
| Number of Residues | 6 |
| Details | binding site for residue GOL B 405 |
| Chain | Residue |
| B | TYR94 |
| B | ALA153 |
| B | ARG156 |
| B | ILE157 |
| B | GOL408 |
| B | HOH647 |
| site_id | AE3 |
| Number of Residues | 2 |
| Details | binding site for residue GOL B 406 |
| Chain | Residue |
| B | PRO99 |
| B | ARG103 |
| site_id | AE4 |
| Number of Residues | 2 |
| Details | binding site for residue GOL B 407 |
| Chain | Residue |
| B | ARG161 |
| B | GOL408 |
| site_id | AE5 |
| Number of Residues | 4 |
| Details | binding site for residue GOL B 408 |
| Chain | Residue |
| B | MET283 |
| B | ASP286 |
| B | GOL405 |
| B | GOL407 |
| site_id | AE6 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 B 409 |
| Chain | Residue |
| B | ARG213 |
| B | ARG216 |
| site_id | AE7 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 B 410 |
| Chain | Residue |
| B | HIS167 |
| B | GLN209 |
| B | ARG216 |
| B | PHE217 |
| site_id | AE8 |
| Number of Residues | 1 |
| Details | binding site for residue SO4 B 411 |
| Chain | Residue |
| B | ARG310 |
| site_id | AE9 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 B 412 |
| Chain | Residue |
| B | ARG163 |
| B | THR165 |
| B | HOH645 |
| site_id | AF1 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 B 413 |
| Chain | Residue |
| A | THR74 |
| B | ASP200 |
| site_id | AF2 |
| Number of Residues | 6 |
| Details | binding site for residue SO4 B 414 |
| Chain | Residue |
| B | THR49 |
| B | VAL51 |
| B | PRO52 |
| B | GLU53 |
| B | PHE81 |
| B | TYR86 |
| site_id | AF3 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 B 415 |
| Chain | Residue |
| B | PRO309 |
| B | ARG310 |
| B | GLY316 |
| B | ASP317 |
| site_id | AF4 |
| Number of Residues | 1 |
| Details | binding site for residue SO4 B 416 |
| Chain | Residue |
| B | ARG4 |
| site_id | AF5 |
| Number of Residues | 5 |
| Details | binding site for residue MG C 401 |
| Chain | Residue |
| C | ASP228 |
| C | 48Y402 |
| C | HOH559 |
| C | HOH593 |
| D | ASP204 |
| site_id | AF6 |
| Number of Residues | 17 |
| Details | binding site for residue 48Y C 402 |
| Chain | Residue |
| C | SER72 |
| C | ARG85 |
| C | ARG88 |
| C | ARG98 |
| C | ARG118 |
| C | TYR125 |
| C | ASP228 |
| C | MG401 |
| C | NAI403 |
| C | HOH556 |
| C | HOH559 |
| C | HOH597 |
| C | HOH598 |
| D | LYS171 |
| D | ASN173 |
| D | VAL174 |
| D | ASP204 |
| site_id | AF7 |
| Number of Residues | 32 |
| Details | binding site for residue NAI C 403 |
| Chain | Residue |
| C | ILE13 |
| C | ALA69 |
| C | ALA70 |
| C | THR71 |
| C | SER72 |
| C | LEU241 |
| C | GLU257 |
| C | VAL259 |
| C | HIS260 |
| C | GLY261 |
| C | SER262 |
| C | ALA263 |
| C | ASP265 |
| C | ILE266 |
| C | ASN273 |
| C | 48Y402 |
| C | HOH534 |
| C | HOH539 |
| C | HOH543 |
| C | HOH570 |
| C | HOH575 |
| C | HOH580 |
| C | HOH598 |
| C | HOH599 |
| C | HOH610 |
| D | ASN173 |
| D | ILE202 |
| D | ASN205 |
| D | MET208 |
| D | GOL403 |
| D | HOH586 |
| D | HOH635 |
| site_id | AF8 |
| Number of Residues | 5 |
| Details | binding site for residue MG C 404 |
| Chain | Residue |
| C | ASP204 |
| D | ASP228 |
| D | 48Y401 |
| D | HOH573 |
| D | HOH574 |
| site_id | AF9 |
| Number of Residues | 8 |
| Details | binding site for residue GOL C 405 |
| Chain | Residue |
| C | MET208 |
| C | MET212 |
| C | ARG213 |
| C | HOH517 |
| D | GLY240 |
| D | LEU241 |
| D | ASP313 |
| D | NAI402 |
| site_id | AG1 |
| Number of Residues | 7 |
| Details | binding site for residue GOL C 406 |
| Chain | Residue |
| C | GLY10 |
| C | HIS15 |
| C | GLU38 |
| C | GLU42 |
| C | THR43 |
| C | ARG46 |
| C | HOH587 |
| site_id | AG2 |
| Number of Residues | 7 |
| Details | binding site for residue GOL C 407 |
| Chain | Residue |
| C | GLY123 |
| C | LEU124 |
| C | LEU175 |
| C | GLN179 |
| C | THR223 |
| C | ASN224 |
| C | LEU225 |
| site_id | AG3 |
| Number of Residues | 2 |
| Details | binding site for residue GOL C 408 |
| Chain | Residue |
| C | TYR94 |
| C | ARG156 |
| site_id | AG4 |
| Number of Residues | 4 |
| Details | binding site for residue GOL C 409 |
| Chain | Residue |
| C | ILE249 |
| C | MET283 |
| C | ASP286 |
| C | GOL410 |
| site_id | AG5 |
| Number of Residues | 4 |
| Details | binding site for residue GOL C 410 |
| Chain | Residue |
| C | VAL115 |
| C | ILE157 |
| C | GOL409 |
| C | HOH648 |
| site_id | AG6 |
| Number of Residues | 4 |
| Details | binding site for residue GOL C 411 |
| Chain | Residue |
| C | PRO99 |
| C | GLU298 |
| C | GOL412 |
| C | HOH613 |
| site_id | AG7 |
| Number of Residues | 9 |
| Details | binding site for residue GOL C 412 |
| Chain | Residue |
| C | PRO99 |
| C | ALA100 |
| C | LYS101 |
| C | ARG103 |
| C | VAL238 |
| C | LEU243 |
| C | PRO245 |
| C | LEU279 |
| C | GOL411 |
| site_id | AG8 |
| Number of Residues | 1 |
| Details | binding site for residue SO4 C 413 |
| Chain | Residue |
| C | ARG213 |
| site_id | AG9 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 C 414 |
| Chain | Residue |
| C | THR121 |
| C | GLU122 |
| C | HOH578 |
| site_id | AH1 |
| Number of Residues | 1 |
| Details | binding site for residue SO4 C 415 |
| Chain | Residue |
| C | ARG310 |
| site_id | AH2 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 C 416 |
| Chain | Residue |
| C | PRO309 |
| C | ARG310 |
| C | GLY316 |
| C | ASP317 |
| C | ALA318 |
| site_id | AH3 |
| Number of Residues | 8 |
| Details | binding site for residue SO4 C 417 |
| Chain | Residue |
| C | PHE80 |
| C | PHE81 |
| C | GLY82 |
| C | ARG85 |
| C | GLU127 |
| D | ASN173 |
| D | VAL174 |
| D | PRO176 |
| site_id | AH4 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 C 418 |
| Chain | Residue |
| C | PRO52 |
| C | GLU53 |
| C | HOH601 |
| site_id | AH5 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 C 419 |
| Chain | Residue |
| C | PRO73 |
| C | THR74 |
| C | ARG75 |
| C | SO4421 |
| site_id | AH6 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 C 420 |
| Chain | Residue |
| C | ARG4 |
| C | GLU33 |
| site_id | AH7 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 C 421 |
| Chain | Residue |
| C | TRP41 |
| C | SO4419 |
| site_id | AH8 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 C 422 |
| Chain | Residue |
| B | LYS269 |
| B | HOH509 |
| C | ASP200 |
| D | THR74 |
| D | HOH541 |
| site_id | AH9 |
| Number of Residues | 17 |
| Details | binding site for residue 48Y D 401 |
| Chain | Residue |
| C | LYS171 |
| C | ASN173 |
| C | VAL174 |
| C | ASP204 |
| C | MG404 |
| D | SER72 |
| D | ARG85 |
| D | ARG88 |
| D | ARG98 |
| D | ARG118 |
| D | TYR125 |
| D | ASP228 |
| D | NAI402 |
| D | HOH520 |
| D | HOH553 |
| D | HOH573 |
| D | HOH574 |
| site_id | AI1 |
| Number of Residues | 30 |
| Details | binding site for residue NAI D 402 |
| Chain | Residue |
| C | ASN173 |
| C | ILE202 |
| C | ASN205 |
| C | MET208 |
| C | GOL405 |
| C | HOH517 |
| C | HOH595 |
| D | ILE13 |
| D | PHE67 |
| D | ALA70 |
| D | THR71 |
| D | SER72 |
| D | ILE84 |
| D | LEU241 |
| D | GLU257 |
| D | HIS260 |
| D | GLY261 |
| D | SER262 |
| D | ALA263 |
| D | ASP265 |
| D | ILE266 |
| D | ASN273 |
| D | 48Y401 |
| D | HOH537 |
| D | HOH541 |
| D | HOH566 |
| D | HOH569 |
| D | HOH589 |
| D | HOH590 |
| D | HOH631 |
| site_id | AI2 |
| Number of Residues | 9 |
| Details | binding site for residue GOL D 403 |
| Chain | Residue |
| C | GLY240 |
| C | LEU241 |
| C | ASP313 |
| C | NAI403 |
| D | MET208 |
| D | MET212 |
| D | ARG213 |
| D | HOH568 |
| D | HOH635 |
| site_id | AI3 |
| Number of Residues | 5 |
| Details | binding site for residue GOL D 404 |
| Chain | Residue |
| D | LEU124 |
| D | GLN179 |
| D | THR223 |
| D | ASN224 |
| D | LEU225 |
| site_id | AI4 |
| Number of Residues | 3 |
| Details | binding site for residue GOL D 405 |
| Chain | Residue |
| D | TYR94 |
| D | ARG156 |
| D | GLY250 |
| site_id | AI5 |
| Number of Residues | 3 |
| Details | binding site for residue GOL D 406 |
| Chain | Residue |
| D | ASP286 |
| D | GLU298 |
| D | GOL407 |
| site_id | AI6 |
| Number of Residues | 4 |
| Details | binding site for residue GOL D 407 |
| Chain | Residue |
| D | VAL97 |
| D | ARG161 |
| D | GOL406 |
| D | GOL408 |
| site_id | AI7 |
| Number of Residues | 3 |
| Details | binding site for residue GOL D 408 |
| Chain | Residue |
| D | ILE249 |
| D | MET283 |
| D | GOL407 |
| site_id | AI8 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 D 409 |
| Chain | Residue |
| D | ARG213 |
| D | ARG216 |
| D | HOH608 |
| site_id | AI9 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 D 410 |
| Chain | Residue |
| D | HIS167 |
| D | GLN209 |
| D | ARG216 |
| D | PHE217 |
| site_id | AJ1 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 D 411 |
| Chain | Residue |
| D | PRO106 |
| D | ARG310 |
| D | HOH633 |
| site_id | AJ2 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 D 412 |
| Chain | Residue |
| B | HOH608 |
| D | ARG89 |
| D | GLU122 |
| D | VAL141 |
| site_id | AJ3 |
| Number of Residues | 5 |
| Details | binding site for residue SO4 D 413 |
| Chain | Residue |
| D | PRO309 |
| D | ARG310 |
| D | GLY316 |
| D | ASP317 |
| D | HOH632 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 20 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:27601325, ECO:0007744|PDB:4YB4 |
| Chain | Residue | Details |
| A | ALA70 | |
| B | ASN273 | |
| C | ALA70 | |
| C | LYS171 | |
| C | ASN173 | |
| C | GLY261 | |
| C | ASN273 | |
| D | ALA70 | |
| D | LYS171 | |
| D | ASN173 | |
| D | GLY261 | |
| A | LYS171 | |
| D | ASN273 | |
| A | ASN173 | |
| A | GLY261 | |
| A | ASN273 | |
| B | ALA70 | |
| B | LYS171 | |
| B | ASN173 | |
| B | GLY261 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 24 |
| Details | BINDING: in other chain => ECO:0000269|PubMed:27601325, ECO:0007744|PDB:4YB4 |
| Chain | Residue | Details |
| A | SER72 | |
| B | ARG98 | |
| B | ARG118 | |
| B | TYR125 | |
| C | SER72 | |
| C | ARG85 | |
| C | ARG88 | |
| C | ARG98 | |
| C | ARG118 | |
| C | TYR125 | |
| D | SER72 | |
| A | ARG85 | |
| D | ARG85 | |
| D | ARG88 | |
| D | ARG98 | |
| D | ARG118 | |
| D | TYR125 | |
| A | ARG88 | |
| A | ARG98 | |
| A | ARG118 | |
| A | TYR125 | |
| B | SER72 | |
| B | ARG85 | |
| B | ARG88 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 12 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:27601325, ECO:0000312|PDB:4YB4 |
| Chain | Residue | Details |
| A | ASP204 | |
| D | ASP204 | |
| D | ASP228 | |
| D | ASP232 | |
| A | ASP228 | |
| A | ASP232 | |
| B | ASP204 | |
| B | ASP228 | |
| B | ASP232 | |
| C | ASP204 | |
| C | ASP228 | |
| C | ASP232 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | SITE: Important for substrate specificity and discrimination against 3-isopropylmalate |
| Chain | Residue | Details |
| A | ARG85 | |
| B | ARG85 | |
| C | ARG85 | |
| D | ARG85 |
